what_the_phage - pharokka integration + chromomap scrollbar fix

Pharokka integration 5f769a05f699a6985ec5135468d0545ebc36ed0c
UKJ cloud compatibility 81bf4400333b792df096051470bda8624ed043ad
computing resources update a0749ba0148866149e8165b0069e4f5053607633
added chromomap scrollbar 588bf210fc104c71287ab561e0837640d0157557
-stub bug when using nextflow version 24.20.4 for syntax check 87ea470ef6c5d069d3c34f30ff41e240fb90ac66

- Nextflow
Published by mult1fractal 12 months ago

what_the_phage - Hotfix_databases

Full Changelog: https://github.com/replikation/WhatthePhage/compare/v1.2.1...v1.2.3

Database fix and sourmash version command change fix

closes 31c241677edf18da4d26bb55d57f2a6b19c523b8, 1d3ed88328f208909a420511bdf7021bef063b5d, 10026f9253c3efef74032ae6743be94a11dc6b0b, d34d428584aace5b2363be1870408d291cc6b3cc, d09808c9c56d31a20f2aac5857d65176032e8d73

- Nextflow
Published by mult1fractal about 2 years ago

what_the_phage - Release v1.2.1

several readme updates (9e307db55dc8da168b9c18abacfe2af21fac9ebe adb5c72f9dea5ee5b5a5b006799442620ce4254f cdcb18658131a3ce5cd74dcc52f51ca075621468 9b5ab3232c503d47c45588116fd0f90e3dd6d7ad)

updated citation (95f334807ff887a9a0f7a2e41b14a0cbbea967aa)

fixed issue #182(f613d87ac2799bee20cd8c83dd07d36fd884741e) fixed issue #183 (165bd3dd6e75da87835b8da46eee6d91a5307d54) and #174 (bcf2fdba010890e468ff7939b1dab4bf40c2bd13) fixed Tab. 2 from p value to score #184 (165bd3dd6e75da87835b8da46eee6d91a5307d54)

- Nextflow
Published by mult1fractal almost 3 years ago

what_the_phage - Release v1.2.0

updated the code for Reviewer comments of Gigascience
fixed #169 59e60210e5ad2ccae9073830d0b04d1be6368e50 and 6e1c50f8bf942cb7b20269d6fd0379cf8ae8b8a3
default run option with tools that were benchmarked 90a0bb81ff439aab7dab5bca27e678aa6db1b54b
user custom database for phage annotation via hmmscan (*.hmm) 1fa19d418b542ea251154774ea123c51d63f6d7d

- Nextflow
Published by mult1fractal over 3 years ago

what_the_phage - Release v1.1.0

correct release number v1.1.0 instead of v.1.1.0 #160

- Nextflow
Published by mult1fractal almost 4 years ago

what_the_phage - Release v1.1.0

WtP generates a summary report (HTML file) #158
- for better user interaction
- summary report contains
- overview (UpSet plot)
- Phage annotations
- CheckV output
- Phage prediction table
- Taxonomic phage classification
code rework (higher modularization) #145
- stub (fast test of channels and modules) #139

- Nextflow
Published by mult1fractal almost 4 years ago

what_the_phage - Pre-release wget_quick_fix v1.0.3

added --no-check-certificate to wget for download_DBs

- Nextflow
Published by mult1fractal about 4 years ago

what_the_phage - Release v1.0.2

Bugfixes fc18d6a2a65e7bf84ed1ce006e7afd0390954447
- Nextflow version not recognized properly when using Nexflow 21.07.xx solved
cloudprofile (dev test atm, some tools not working, )
- will be added in a future major release

Virsorter2 update from @papanikos * split vs2 db download to separate module a29c0e643c7ae84af7de3e912dc7564d46f2d9d4 * update all virsorter2 tasks with db 04426ed70c75da916704e0129393cf76f69ab4d1 * update virsorter2 module 6dea944f48eb19feeb0fc2b73163873289f5f39c * be more explicit on dir names 3f2750ab69d374921e96b4c478857556f8ba3f17 * rename for coherence with other dbs 482aad6957dbed4ee8b6fe230c746068856c45d8 * handle vs2 in the main workflow 7b5fb339909bc4b775e8cd903dc6eccb7227ecca * update image tag f8b7ec04a985b48e20573f47bcaa495dbc9a88c6

Marvel Update from @papanikos 5efc9f67d85e4f0d55068c7c3d4e298fb4ae37db

- Nextflow
Published by mult1fractal over 4 years ago

what_the_phage - Release v1.0.1

added virsorter2 to local and node config, also gave virnet more cores 4d9ffa2b8a829feac6c63e5bc1414819a1f28898
closes #123

- Nextflow
Published by mult1fractal about 5 years ago

what_the_phage - Release v1.0.0 [NEXTFLOW version 20.07.1]

contains two new tools
- Virsorter 2beta a9b5ee4d840fcd30c43aaadabebdc6ab780cfbd0
- Seeker (thanks @papanikos ) 1e2be4ef1f87419a071063f60f42a6b925e86de8 cd5681ddd0de20734ca21d47f050a8a4a2f84679
resolved some minor issues for v1.0.0 (code readability) c690c2204add69b24494ddf309545537bf3b0738
updated the Readme 420815c3ccc6fac259ebc5cd130bef33a549ffc9
- read-the-docs documentation

- Nextflow
Published by mult1fractal over 5 years ago

what_the_phage - Release v0.9.0 [NEXTFLOW version 20.07.1]

New Tool Integration: Phigaro d675d96d81bfdec8e8e54719e1c7216860b1906e
- added our own Phigaro-Docker to the container.config file (maintanance reasons for dockerhub) 2c071f1251b19561be42ba56cd87d327d1447406
Integrated a new testprofile for a faster testrun: -profile local,smalltest,docker 58754862fdc955db9c5c75782335b172ede84da5
- this testprofile runs the test-data/all_pos_phage.fa dataset
- updated Readme with the smalltest profile and runtime and WtP simple flow chart from preprint fbde9e8ec568fe3207428f45770ff885640862f3
fixed name changing input contigs by Vibrant d675d96d81bfdec8e8e54719e1c7216860b1906e
added a version control header 58754862fdc955db9c5c75782335b172ede84da5
added max cores for local runs 8a1476eaa89ee6718dd3b23e8d9fbac4c89f5be8
Update setup_container.nf 7725fd8f9848cb6c8bcb018ac40186281d8988c5

- Nextflow
Published by mult1fractal over 5 years ago

what_the_phage - Release v0.8.2 [NEXTFLOW version 20.01.0 & 20.04.1 & 20.07.1]

small update * updated Dockerfiles with procps as suggested in #89 0cab85f * WtP results contain now execution report and execution timeline 0cab85f * added Citations.bib for easy citation (import this file into your citation program) cdea715 * contains references of all tools we use * stored in results/literature/Citations.bib

- Nextflow
Published by mult1fractal over 5 years ago

what_the_phage - Release v0.8.1 [NEXTFLOW version 20.01.0 & 20.04.1]

Small update * update sourmash version to 3.4.1 and better DB handling (#87) * Readme update to include the WtP pre-print info

- Nextflow
Published by replikation over 5 years ago

what_the_phage - Release v0.8.0 [NEXTFLOW version 20.01.0 & 20.04.1]

reduced the rate of false-positive phage contigs via improving several result cutoffs #86 #80
- also some cutoffs can now be modified by the user via params
- e.g: --dv_filter p-value cut-off [default: 0.9]
- check --help for more Infos
added virome mode to vibrant and virsorter #81
- both modes are executed and clearly labelled as such
- virome mode (takes more time) can be deactivated via adding --virome
- we recommend in not deactivating it as you get more information with both methods on
slurm Executer implementation and more singularity tests #84
- thanks to @mshamash for testing the WtP code
heatmap visual now scales correctly with the number of contigs and tools #83
fixed some blast DB distribution bugs af9099c
a test profile was included #83
- just add test to the profile e.g. -profile test,slurm,singularity
- uses 8 assembly files, takes around ~10h on a 24 threads computer
fixed bugs of WtP not recognising pre-downloaded databases 87b8c25c830a102dc755e87cb2572869f9d51c2f

- Nextflow
Published by replikation over 5 years ago

what_the_phage - Release v0.7.1 [NEXTFLOW version 20.01.0]

small release tackling to remove a critical issue with vibrant 3ffd53554e66e539ede031bddc091472d3305b89
fixed #78 display of results from tax. classification
- shows now ("no match") when no phage was assigned to a contig
fixed chromomap error 5cb02a472e9f81f05915f6ebb85fce55cf2afba1

- Nextflow
Published by mult1fractal over 5 years ago

what_the_phage - Release v0.7: checkV, tax, QoL

We improved the analysis results after all the phage contig identification steps. With the chromomap annotation, checkV and the sourmash taxonomy you should get a really good idea about each phage predicted contig.

In Detail:

checkV implementation on positive phage contigs (#70)
phage identification or annotation can be skipped (#68)
- e.g. you only want to generate fancy annotation plots
updated the readme heavily (#72)
some fixes towards long read .fastq input (b6056f2d3c88e8db6da53fedf47cf2d71b48446a)
- it generates tables etc. but is not optimized
- We focus on that next release
- it's working, but too many false positive hits, however, with the annotation data etc. its easy to manually validate what's positive
sourmash taxonomic classification added to positive contigs (#71)
- you will know if your phage is similar to a described one

- Nextflow
Published by replikation over 5 years ago

what_the_phage - Release v0.6: Phage annotation, Singularity and more

As always run a specific release via nextflow run replikation/What_the_Phage -r v0.6 --help

implemented annotation and visualization of positive contigs #62 #57
- hmmscan, prodigal
length filter is included as fragments below 1500 bp are usually false-positive #59
singularity was implemented #61
various bug fixes
--setup flag to pre-download container (docker/singularity) and databases
unified params for e.g. --database --cachedir
improved --help and Readme
implemented a -profile Executers,Engines (see --help ) to better merge and support various profiles
- e.g. -profile local,docker or ebi,singularity

- Nextflow
Published by replikation almost 6 years ago